crossing96/oncoscreening huggingface dataset:
Comparison of bladder carcinogenesis biomarkers in the urine of traditional cigarette users and e-cigarette users.	BACKGROUND: During the use of electronic cigarettes (e-cigarettes), users are still exposed to carcinogens similar to those found in tobacco products. Since these carcinogens are metabolized and excreted in urine, they may have carcinogenic effects on the bladder urinary tract epithelium. This meta-analysis aimed to compare bladder cancer carcinogens in the urine of tobacco users and e-cigarette users using a large number of samples. METHODS: A systematic meta-analysis was performed using data obtained from several scientific databases (up to November 2023). This cumulative analysis was performed following the Preferred Reporting Items for Systematic Evaluation and Meta-Analysis (PRISMA) and Assessing the Methodological Quality of Systematic Evaluations (AMSTAR) guidelines, according to a protocol registered with PROSPERO. This study was registered on PROSPERO and obtained the unique number: CRD42023455600. RESULTS: The analysis included 10 high-quality studies that considered polycyclic aromatic hydrocarbons (PAHs), volatile organic compounds (VOCs) and tobacco-specific nitrosamines (TSNAs). Statistical indicators show that there is a difference between the tobacco user group and the e-cigarette user group in terms of 1-Hydroxynaphthalene (1-NAP) [weighted mean difference (WMD)10.14, 95% confidence interval (CI) (8.41 to 11.88), p < 0.05], 1-Hydroxyphenanthrene (1-PHE) [WMD 0.08, 95% CI (-0.14 to 0.31), p > 0.05], 1-Hydroxypyrene (1-PYR) [WMD 0.16, 95% CI (0.12 to 0.20), p < 0.05], 2-Hydroxyfluorene (2-FLU) [WMD 0.69, 95% CI (0.58 to 0.80), p < 0.05], 2-Hydroxynaphthalene (2-NAP) [WMD 7.48, 95% CI (4.15 to 10.80), p < 0.05], 3-Hydroxyfluorene (3-FLU) [WMD 0.57, 95% CI (0.48 to 0.66), p < 0.05], 2-Carbamoylethylmercapturic acid (AAMA) [WMD 66.47, 95% CI (27.49 to 105.46), p < 0.05], 4-Hydroxy-2-buten-1-yl-mercapturic acid (MHBMA) [WMD 287.79, 95% CI (-54.47 to 630.04), p > 0.05], 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNAL) [WMD 189.37, 95% CI (78.45 to 300.29), p < 0.05], or N0-nitrosonornicotine (NNN) [WMD 11.66, 95% CI (7.32 to 16.00), p < 0.05]. CONCLUSION: Urinary bladder cancer markers were significantly higher in traditional tobacco users than in e-cigarette users.Systematic review registration: PROSPERO (CRD42023455600: https://www.crd.york.ac.uk/PROSPERO/).	bladder
Effectiveness and Safety of Extended Lymph Node Dissection during Radical Surgery in Patients with Bladder Cancer: A Meta-Analysis.	OBJECTIVE: Bladder cancer (BC) is the most common malignant tumour of the urinary system, and radical cystectomy combined with pelvic lymph node dissection (LND) is the standard treatment for BC. We conducted this meta-analysis to explore the efficacy and safety of extended lymph node dissection in radical cystectomy for BC. METHODS: PubMed, Embase, ProQuest PsycINFO, CINAHL, Web of Science and The Cochrane Library databases were searched for studies on extended lymph node dissection during radical BC surgery. The search time limit was from the establishment of the database to December 2023. Screening and quality assessment of literature were conducted. This meta-analysis was conducted to evaluate the influence of different lymph node dissection methods on recurrence-free survival (RFS), overall survival (OS), operation time, 90-day readmission rate and postoperative complication rate. RESULTS: A total of 15 studies were included, including 4854 patients. All studies were of high quality. This meta-analysis showed no statistically significant difference in the operation time, postoperative complications and 90-day hospitalisation rate between the two groups of patients. The harvested volume of lymph nodes, RFS and OS rate were not statistically different. CONCLUSIONS: Among patients with BC undergoing radical cystectomy, extended lymph node dissection did not have a significant effect on operative time, 90-day readmission rates or postoperative complication rates. Thus, extended lymph node dissection is a safe treatment that does not increase the patient's surgical risk.	bladder
Predicting bladder cancer survival with high accuracy: insights from MAPK pathway-related genes.	The mitogen-activated protein kinase (MAPK) pathway plays a critical role in tumor development and immunotherapy. Nevertheless, additional research is necessary to comprehend the relationship between the MAPK pathway and the prognosis of bladder cancer (BLCA), as well as its influence on the tumor immune microenvironment. To create prognostic models, we screened ten genes associated with the MAPK pathway using COX and least absolute shrinkage and selection operator (LASSO) regression analysis. These models were validated in the Genomic Data Commons (GEO) cohort and further examined for immune infiltration, somatic mutation, and drug sensitivity characteristics. Finally, the findings were validated using The Human Protein Atlas (HPA) database and through Quantitative Real-time PCR (qRT-PCR). Patients were classified into high-risk and low-risk groups based on the prognosis-related genes of the MAPK pathway. The high-risk group had poorer overall survival than the low-risk group and showed increased immune infiltration compared to the low-risk group. Additionally, the nomograms built using the risk scores and clinical factors exhibited high accuracy in predicting the survival of BLCA patients. The prognostic profiling of MAPK pathway-associated genes represents a potent clinical prediction tool, serving as the foundation for precise clinical treatment of BLCA.	bladder
Risk factors for failing to complete gemcitabine-cisplatin neoadjuvant chemotherapy in muscle invasive bladder cancer patients.	PURPOSE: We evaluated the risk factors associated with failure to complete gemcitabine-cisplatin (GP) neoadjuvant chemotherapy (NAC) for muscle-invasive bladder cancer (MIBC). MATERIALS AND METHODS: In total, 231 patients with MIBC treated with NAC before undergoing radical cystectomy between 2013 and 2022 participated in this study. Logistic regression analysis was performed to assess the relationship between the likelihood of incomplete NAC and clinical and demographic variables, including age, sex, hypertension (HTN), diabetes mellitus (DM), prechemotherapy glomerular filtration rate, clinical T stage, clinical N stage, and body mass index (BMI). RESULTS: Of 231 patients, 209 (90.5%) and 22 (9.5%) completed and discontinued the NAC course, respectively. The mean age was 66.13±9.15, 65.63±9.07, and 70.86±8.66 years for the total sample, continuation, and discontinuation groups, respectively (p=0.010). No significant inter-group differences in sex, HTN, height, weight, BMI, pre-chemotherapy glomerular filtration rate, clinical T stage, or clinical N stage were observed. According to the results of the multivariable analysis, age (odds ratio [OR] 1.076, 95% confidence interval [CI] 1.013-1.143, p=0.018) and the presence of DM (OR 2.541, 95% CI 1.028-6.281, p=0.043) were significantly associated with NAC discontinuation. CONCLUSIONS: Thus, older age and presence of DM are potential risk factors for GP NAC discontinuation in patients with MIBC. Further studies are required to validate our findings and develop strategies to minimize the rate of GP NAC discontinuation in this population.	bladder
MH2AFormer: An Efficient Multiscale Hierarchical Hybrid Attention With a Transformer for Bladder Wall and Tumor Segmentation.	Achieving accurate bladder wall and tumor segmentation from MRI is critical for diagnosing and treating bladder cancer. However, automated segmentation remains challenging due to factors such as comparable density distributions, intricate tumor morphologies, and unclear boundaries. Considering the attributes of bladder MRI images, we propose an efficient multiscale hierarchical hybrid attention with a transformer (MH2AFormer) for bladder cancer and wall segmentation. Specifically, a multiscale hybrid attention and transformer (MHAT) module in the encoder is designed to adaptively extract and aggregate multiscale hybrid feature representations from the input image. In the decoder stage, we devise a multiscale hybrid attention (MHA) module to generate high-quality segmentation results from multiscale hybrid features. Combining these modules enhances the feature representation and guides the model to focus on tumor and wall regions, which helps to solve bladder image segmentation challenges. Moreover, MHAT utilizes the Fast Fourier Transformer with a large kernel (e.g., 224 × 224) to model global feature relationships while reducing computational complexity in the encoding stage. The model performance was evaluated on two datasets. As a result, the model achieves relatively best results regarding the intersection over union (IoU) and dice similarity coefficient (DSC) on both datasets (Dataset A: IoU = 80.26%, DSC = 88.20%; Dataset B: IoU = 89.74%, DSC = 94.48%). These advantageous outcomes substantiate the practical utility of our approach, highlighting its potential to alleviate the workload of radiologists when applied in clinical settings.	bladder
The Missing Trial Variable: A Case Report on Dietary Modification in a Patient with Durable Complete Remission After an Immunotherapy Clinical Trial for Metastatic Bladder Cancer.	A patient with metastatic bladder cancer has had an ongoing 9-year complete remission on a clinical trial of immunotherapy with nivolumab and ipimumab, but he also was following an intensive dietary and nutritional supplement regimen. Whether this combination or the immunotherapy alone brought about his good outcome is unknown but could be clarified in future trials by improved data collection about dietary and supplement choices.	bladder
A Multicenter Prospective Randomized Controlled Trial Comparing Cxbladder Triage to Cystoscopy in Patients With Microhematuria: The Safe Testing of Risk for Asymptomatic Microhematuria Trial.	"PURPOSE: AUA guidelines for patients with microhematuria (≥3 red blood cells [RBC]/high-power field [hpf]) include cystoscopy for most over age 40 due to risk of urothelial cancer (UC). Cxbladder Triage (CxbT) is a urinary genomic test with UC negative predictive value of 99%. In this prospective randomized controlled trial, we compared cystoscopy use in a standard of care (SOC) arm vs a marker-based approach. MATERIALS AND METHODS: All patients with hematuria provided urine for a CxbT. Those categorized as lower risk (LR), defined as 3 to 29 RBC/hpf and minimal smoking history (<10 pack-years) were randomized between the test group provided with the CxbT result vs the SOC control group. Negative CxbT patients were offered omission of cystoscopy with surveillance. ""Not lower risk"" (NLR) patients (>30 RBC/hpf or >10 pack-year smoking history) had a CxbT but otherwise SOC. Patient decision and outcomes were recorded. RESULTS: Of 390 eligible patients, 255 were NLR and 135 were LR randomized to CxbT informed decision or SOC. The median age was 62 years (range 18-94) and 54% were male. Overall, 63% of CxbT tests were negative. For NLR patients, 82% had cystoscopy. In the LR control group, cystoscopy was performed in 67% of SOC and 27% in the test group (relative risk 0.41 [95% CI 0.27-0.61]). Compared to cystoscopy, CxbT had 90% sensitivity, 56% specificity, and 99% negative predictive value for UC. CONCLUSIONS: In this prospective randomized controlled trial, use of CxbT in patients with LR hematuria resulted in 59% reduction of cystoscopy use. This clinical utility of CxbT can reduce the burden of unnecessary cystoscopies."	bladder
A surgical checklist for optimizing the quality and outcomes of transurethral resection of bladder tumors: A literature review.	To preserve the bladder without compromising survival, further treatments need to be optimized to prevent the recurrence and progression of non-muscle invasive bladder cancer. In clinical practice, transurethral resection of bladder tumors is essential for bladder cancer management. The primary goal of surgery is to achieve accurate pathological evaluation and complete resection of bladder cancer; high resection quality is required for the procedure. A representative surrogate indicator of the resection quality is the presence of the detrusor muscle in the resection specimen. Therefore, complete visual resection of bladder cancer with a muscle layer is crucial for decreasing the recurrence and progression rates of non-muscle-invasive bladder cancer. However, this procedure is complex and requires sufficient experience and knowledge to be performed thoroughly, safely, and efficiently. Surgical checklists represent an approach to filling the knowledge and experience gaps and improving the quality and safety of surgery. By checking items during transurethral resection, it is expected that the recording of risk factors related to recurrence and progression will improve, the rate of visually complete resection with muscles will increase, and the rate of intravesical recurrence will decrease. The simplicity of checklists is an additional benefit. In recent years, surgical checklists have received increasing attention in order to achieve high-quality resections and reduce disparities between surgeons and institutions. This literature review outlines the evolving treatment strategies for patients with non-muscle-invasive bladder cancer, focusing on surgical checklists for the transurethral resection of bladder tumors.	bladder
New synergistic combination therapy approaches with HDAC inhibitor quisinostat, cisplatin or PARP inhibitor talazoparib for urothelial carcinoma.	Urothelial carcinoma (UC) urgently requires new therapeutic options. Histone deacetylases (HDAC) are frequently dysregulated in UC and constitute interesting targets for the development of alternative therapy options. Thus, we investigated the effect of the second generation HDAC inhibitor (HDACi) quisinostat in five UC cell lines (UCC) and two normal control cell lines in comparison to romidepsin, a well characterized HDACi which was previously shown to induce cell death and cell cycle arrest. In UCC, quisinostat led to cell cycle alterations, cell death induction and DNA damage, but was well tolerated by normal cells. Combinations of quisinostat with cisplatin or the PARP inhibitor talazoparib led to decrease in cell viability and significant synergistic effect in five UCCs and platinum-resistant sublines allowing dose reduction. Further analyses in UM-UC-3 and J82 at low dose ratio revealed that the mechanisms included cell cycle disturbance, apoptosis induction and DNA damage. These combinations appeared to be well tolerated in normal cells. In conclusion, our results suggest new promising combination regimes for treatment of UC, also in the cisplatin-resistant setting.	bladder
Natural History and Genomic Landscape of Chemotherapy-Resistant Muscle-Invasive Bladder Cancer.	PURPOSE: Patients with residual invasive bladder cancer after neoadjuvant chemotherapy (NAC) and radical cystectomy have a poor prognosis. Data on adjuvant therapy for these patients are conflicting. We sought to evaluate the natural history and genomic landscape of chemotherapy-resistant bladder cancer to inform patient management and clinical trials. METHODS: Data were collected on patients with clinically localized muscle-invasive urothelial bladder cancer treated with NAC and cystectomy at our institution between May 15, 2001, and August 15, 2019, and completed four cycles of gemcitabine and cisplatin NAC, excluding those treated with adjuvant therapies. Survival was estimated using the Kaplan-Meier method, and multivariable Cox proportional hazards models were used to identify predictors of recurrence-free survival (RFS). Genomic alterations were identified in targeted exome sequencing (Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets) data from post-NAC specimens from a subset of patients. RESULTS: Lymphovascular invasion (LVI) was the strongest predictor of RFS (hazard ratio, 2.15 [95% CI, 1.37 to 3.39]) on multivariable analysis. Patients with ypT2N0 disease without LVI had a significantly prolonged RFS compared with those with LVI (70% RFS at 5 years). Lymph node yield did not affect RFS. Among patients with sequencing data (n = 101), chemotherapy-resistant tumors had fewer alterations in DNA damage response genes compared with tumors from a publicly available chemotherapy-naïve cohort (15% v 29%; P = .021). Alterations in CDKN2A/B were associated with shorter RFS. PIK3CA alterations were associated with LVI. Potentially actionable alterations were identified in more than 75% of tumors. CONCLUSION: Although chemotherapy-resistant bladder cancer generally portends a poor prognosis, patients with organ-confined disease without LVI may be candidates for close observation without adjuvant therapy. The genomic landscape of chemotherapy-resistant tumors is similar to chemotherapy-naïve tumors. Therapeutic opportunities exist for targeted therapies as adjuvant treatment in chemotherapy-resistant disease.	bladder
Grade Heterogeneity in High-Grade Urothelial Carcinomas: Does It Have an Impact on the Survival of Patients With Intermediate/High-Risk Nonmuscle-Invasive Bladder Cancer Who Received Adequate Adjuvant Bacillus Calmette-Guérin Therapy?	PURPOSE: We aimed to compare recurrence-free survival (RFS) and progression-free survival (PFS) of the patients with pure high-grade (HG) vs mixed-grade (MG) nonmuscle-invasive bladder cancer who received adequate bacillus Calmette-Guérin therapy. MATERIALS AND METHODS: We conducted a retrospective cohort analysis using data from an institutional database. The study included patients diagnosed with HG nonmuscle-invasive bladder cancer at the initial transurethral resection specimen between 2010 and 2020. The initial transurethral resection specimens of all patients were reevaluated by a dedicated uropathologist. The percentage of low-grade tumor areas accompanying HG areas was determined for each case. Time-to-event analysis was performed using the Kaplan-Meier method. RFS and PFS rates were compared between groups. RESULTS: Of the 203 patients enrolled in the study, 69 (34%) had MG tumors. Recurrence was observed in 41 out of 134 patients (30.6%) in the HG group and in 19 out of 69 patients (27.5%) in the MG group. The 36-month RFS rates were 69% (CI: 62-77) and 72% (CI: 62-83) for the HG-urothelial carcinoma (UC) and MG-UC groups, respectively. The RFS rates were similar between groups (log-rank, P = .58). Progression was observed in 22 out of 134 patients (16.4%) in the HG group and in 4 out of 69 patients (5.8%) in the MG group. The 36-month PFS rates were 84% (CI: 77-90) and 94% (CI: 89-100) for the HG-UC and MG-UC groups, respectively. The pure HG-UC group had a worse PFS than the MG-UC group (log-rank, P = .042). Multivariate analysis demonstrated that age and tumor grade were significant risk factors for the development of progression. CONCLUSIONS: The indication of MG-UC category separately from pure HG carcinomas in the pathology report seems to be an important issue that can guide patient management. In this way, both more accurate risk classification and more accurate patient counseling can be performed. More importantly, the treatment plan can be made more accurately. For more precise conclusions, our results should be supported by prospective studies with larger sample size.	bladder
Incidence and management of prostatic urethra recurrence in a cohort of 21 patients who received BCG induction for non-muscle invasive bladder cancer.	PURPOSE: To describe the incidence and management of patients who develop a prostatic urethral (PU) urothelial carcinoma recurrence after Bacillus Calmette-Guerin (BCG) induction for non-muscle invasive bladder cancer (NMIBC). MATERIALS AND METHODS: We performed a retrospective cohort study of all patients who received BCG induction at our institution from 1996 to 2021 (N = 642) for NMIBC. All patients with pathologically confirmed PU involvement following BCG induction with no known PU involvement pre-BCG were included. We describe the presentation, management, and outcomes for PU recurrence. RESULTS: Among the 642 patients, 21 (3.3%) patients had a PU recurrence after BCG induction. 8 (38%) patients received >2 cycles of BCG induction prior to the recurrence. Median time from induction to PU recurrence was 21 months and 12 (57.1%) patients had concurrent bladder recurrence. At the time of their PU recurrence, 14/21 (67%) of patients were deemed BCG Unresponsive. Nearly all (18/21) were high grade, and 10 were stage Tis, 7 Ta, and 3 T1, and 1 T2. 19/21 (90%) patients received bladder sparing treatment: 6 with TURBT and BCG, 6 with TURBT and intravesical chemotherapy, 5 with TURBT only, and 2 did not receive immediate treatment of their PU recurrence due to advanced stage of disease. 2/21 (9.5%) received a radical cystectomy for initial treatment of the post-BCG PU recurrence, of which all were >pT2. Median follow-up time from BCG induction to the patient's last visit was 64.5 months. Following treatment of PU recurrence, 15/18 patients had another recurrence at a median of 5 months: about 47% of recurrences were bladder only and 14% recurred only in the PU as well. About 1 patient received a RC after the second recurrence and was pT2. CONCLUSION: Patients with PU recurrences following intravesical BCG have a high-risk disease phenotype with a significant risk of recurrence. Conservative management may be appropriate for well-selected patients who do not desire a cystoprostatectomy.	bladder
Cystectomy for bladder cancer in Sweden - short-term outcomes after centralization.	OBJECTIVE: Radical cystectomy (RC) for bladder cancer is associated with an inherent risk of complications and even postoperative mortality. The number of hospitals performing RC has decreased in Sweden over time, and since a formal regional centralization in 2017 cystectomy care is currently provided by nine hospitals. MATERIAL AND METHODS: In the Swedish National Urinary Bladder Cancer Register (SNRUBC) 90-day complications after RC have been registered with high coverage since 2012. Descriptive data and short-term outcomes were compared in relation to centralization of the cystectomy care by stratifying data before (2012-2016) and after (2017-2023). RESULTS: Out of all 4,638 cystectomies, 2,738 (59%) were performed after the centralization in 2017 and onwards. The median age at RC increased from 71 (Inter Quartile Range [IQR] 65-76) to 73 (IQR 67-77) years, and the proportion of patients with comorbidity (American Society of Anesthesiologists [ASA] 3 or 4) increased from 32% to 37% after the centralization (p < 0.001). The number of patients suffering from high-grade complications within 90 days of surgery corresponding to Clavien grade three were 345 (18%) and 407 (15%), and corresponding to Clavien grade four 61 (3%) and 64 (2%) before and after centralization, respectively. Reoperations within 90 days of RC decreased from 234/1,900 (12%) to 208/2,738 (8%) (p < 0.001), and 90-day mortality decreased from 84/1,900 (4%) to 85/2,738 (3%) (p = 0.023) before and after centralization, respectively. CONCLUSION: After the centralization of the cystectomy-care in Sweden, older patients and individuals with more extensive comorbidity were offered RC whereas 90-day mortality and the proportion of patients subjected to reoperations within 90 days of surgery decreased without increasing waiting times.	bladder